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  • Renaming fasta headers - string within a string issue

    Hi Everyone,

    I am in the midst of renaming some fasta headers to include the chromosomes they have been mapped to (from a tab delimited txt file). I don't have any problems setting up the hash for the scaffold and chromosome locations...the problem is that I have some short strings contained in longer strings (scaffold1 and scaffold10 and scaffold100). Usually I would add "$" to the end of my search term (/scaffold1$/) and thereby indicate the end of the search string, but I'm not sure how to make use of this when the search term is a variable ($hash{$scaff/$/}). Advice?

    Below is my script so far...and TIA!

    Code:
    #!/bin/bash/perl
    #mod-header2include-chrom.pl
    #This script is intended to read in a fasta file and a tab-delimited file and use the information from the tab-delimited file to modify the header.
    #In this case, we are appending to the header (e.g. "scaffold671") the chromosome to which it has been mapped and the number of genes on this scaffold.
    
    use strict;
    use warnings;
    
    open (DATA, "<genome-assoc-chromosomes.txt") or die "Could not open genome chromosome mapping data: $!\n";
    open (FASTA, "<scafSeq.FG.fill") or die "Could not open Fasta file: $!\n";
    
    my %hash;
    
    while (<DATA>)
    {
    chomp;
    if ($_ =~ "scafold"){ #skip header - scafold is spelled incorrectly on purpose;
    next;
    }
    else {
    my ($key, $chrom, $len, $gene) = split /\t/;
    $hash{$key} = $chrom;
    }
    }
    
    while (<FASTA>){
    
    my $line = $_;
    chomp ($line);
    if ( defined $hash{$line} ) {
    print "$line-$hash{$line}";
    }
    else { print $line; }
    
    }

  • #2
    Hi,
    Kindly upload a sample of both files (scafSeq.FG.fill and genome-assoc-chromosomes.txt). Without the fasta file, I am wondering how the following:
    while (<FASTA>){
    my $line = $_;
    chomp ($line);
    if ( defined $hash{$line} ) {


    reads in the header line with ">" from "<scafSeq.FG.fill"

    does the variable $key in "$hash{$key} = $chrom;" contain ">"?

    Comment

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